If we are talking super thin New York style pizza versus stuffed Chicago pan style pizza then New York style takes it. However, there are plenty of joints in Chicago that serve it up New York style. Giggios in Evanston is one excellent example.

If New York style is synonymous with thin crust pie cut and Chicago style is synonymous with deep dish, then NY Style wins. But I can get great thin crust in Chicago, no problem. But it's way easier in NYC, especially if you are after just a slice to go and not going to sit down for a pie.

( I didn't read EPT's post as I was writing mine, although it loks like it. )

I am a glutton. I fear no lipids, but Chicago-style pizza is just too fucking much.
A fucking mouthful of mediocre mozzarella. No thanks.

I like some deep dish, like Pequod's, but the standard tomato-topped Chicago heart attack pie, fuck off.

New York.

I'm not seeing much of either these days, it's mostly Spacca Napoli for me.

edit: Just noticed that the question is not on style, but location. Chicago has several styles and each is done very well. This city takes its pizza very seriously. I retract my vote and give it to the home team.

A few thoughts from Dan Lepard, perhaps the best baker in the UK, regarding the perfect pizza:

But the perfect pizza is another creature altogether, as rare as a sexy politician or a footballer with opinions on the works of Proust. I asked Lepard what he thought makes for this quasi-mythical food item. 'Flour, time and Italians,' he said. 'British flour is designed to be moist and heavy, because that's what we want for our tin loaves. To make a good pizza you need proper Italian double zero. Then you need to make the dough early and leave it to rise for a few hours. And the final thing is the people who make it. They have to be Italian.'

I'm sadly unfamiliar with either style but the one closest to that wins. Generally speaking, anything other than a thin crust is an abomination.

I love them both and crave them at separate times. I'll never understand the vitriol NY style lovers have against Chicago style. In the majority, the New Yorkers I've met get downright offended by the idea of Chicago style pizza. I just don't understand.

For a lunch, a poker break, or a midnight snack, a thin slice is hard to top. But there are better ingredients and more flavors involved in Chicago-style.